Variant report

Variant	rs2300033
Chromosome Location	chr7:108006941-108006942
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:107991896..107993618-chr7:108006610..108008809,2	MCF-7	breast:
2	chr7:107997597..108000598-chr7:108005435..108008873,4	MCF-7	breast:
3	chr7:108006500..108008005-chr7:108054331..108056945,2	MCF-7	breast:
4	chr7:108000928..108003876-chr7:108005996..108008885,2	MCF-7	breast:
5	chr7:107934022..107936872-chr7:108006050..108008513,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266112	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10487846	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs10487849	0.84[ASW][hapmap];0.87[CEU][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs10487851	0.83[CEU][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs10953562	0.84[ASW][hapmap];0.87[CEU][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs10953564	0.84[EUR][1000 genomes]
rs12056165	0.84[EUR][1000 genomes]
rs12154914	0.84[EUR][1000 genomes]
rs12669401	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12669405	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17418660	0.84[ASW][hapmap];0.87[CEU][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs17419000	0.84[ASW][hapmap];0.87[CEU][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs17419221	0.87[CEU][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs17419906	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2267882	0.84[ASW][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap]
rs2267886	0.82[CEU][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs2284285	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2300015	0.82[YRI][hapmap]
rs2300016	0.86[CEU][hapmap];1.00[YRI][hapmap]
rs2300028	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2300032	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2300034	0.81[CHB][hapmap];0.85[CHD][hapmap];0.81[ASN][1000 genomes]
rs4727709	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56056000	0.84[EUR][1000 genomes]
rs60830378	0.84[EUR][1000 genomes]
rs62469223	0.84[EUR][1000 genomes]
rs62469224	0.85[EUR][1000 genomes]
rs62469225	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66526866	0.83[EUR][1000 genomes]
rs67033131	0.84[EUR][1000 genomes]
rs67652370	0.84[EUR][1000 genomes]
rs68029971	0.85[EUR][1000 genomes]
rs6942944	0.84[EUR][1000 genomes]
rs6967405	0.87[CEU][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs7784390	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs7789982	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv831090	chr7:107786650-108011196	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv888942	chr7:107893695-108055858	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv888943	chr7:107893695-108058574	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1030425	chr7:107910716-108041036	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2300033	LHFPL3	cis	cerebellum	SCAN
rs2300033	NRCAM	Cis_1M	lymphoblastoid	RTeQTL
rs2300033	NRCAM	cis	lymphoblastoid	seeQTL
rs2300033	LHFPL3	cis	parietal	SCAN
rs2300033	RINT1	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107992600-108007400	Weak transcription	HUVEC	blood vessel
2	chr7:107999200-108008800	Weak transcription	Brain Anterior Caudate	brain
3	chr7:107999200-108011200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr7:107999600-108009000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr7:108000000-108008400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr7:108000000-108008400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr7:108004000-108016600	Weak transcription	Pancreas	Pancrea
8	chr7:108004400-108007200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:108004400-108016600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr7:108006800-108007200	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr7:108006800-108007200	Enhancers	A549	lung

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